Cerro Largo Fútbol Club was established as recently as November 2002, in the city of Melo. As a result, they are the youngest team currently competing in Uruguay's top flight and one of the youngest teams in the country. Despite the team's youth, Cerro Largo have already attracted a significant fan base, as they are the only professional club representing the Cerro Largo Department.

During their short history, the team have made a rapid ascent through the league system. At the end of the 2007-08 season, Cerro Largo gained promotion to the Primera División for the first time, by virtue of their 2nd place finish in the Segunda División. Their initial stay in the top tier lasted for two full seasons, before the club suffered relegation back to the Segunda División.

Fortunately, the team's stay in the second tier was short-lived. At the conclusion of the 2010–11 campaign, Cerro Large defeated Club Atlético Boston River in a playoff game to once again earn promotion to the Primera División. The 2011-12 season brought about the team's best domestic performance to date, as they finished 5th in both the Apertura and Clausura competitions, giving them a 4th place finish overall. As a result of this high finish, they gained entry to their first ever major international competition, the 2012 Copa Sudamericana, thereby further increasing the team's status.

Some of the club's most notable players have included striker Sebastián Sosa, whose performances in the 2011-12 season earned him a transfer to Serie A side, Palermo; as well as current star and hometown hero, Bruno Silva, was born in Cerro Largo and is a former Uruguayan international defender.

The team's home matches are staged at the Estadio Arquitecto Antonio Eleuterio Ubilla. It is currently able to hold a maximum of 9,000 spectators.